Microfluidic system for amplifying and detecting polynucleotides in parallel

Abstract

The present technology provides for an apparatus for detecting polynucleotides in samples, particularly from biological samples. The technology more particularly relates to microfluidic systems that carry out PCR on nucleotides of interest within microfluidic channels, and detect those nucleotides. The apparatus includes a microfluidic cartridge that is configured to accept a plurality of samples, and which can carry out PCR on each sample individually, or a group of, or all of the plurality of samples simultaneously.

The invention claimed is: 
     
       1. A fully automated, continuous random-access molecular diagnostic test system comprising:
 a plurality of consumables comprising:
 a plurality of multi-sample microfluidic cartridges, each microfluidic cartridge comprising a plurality of separate sample inlets, each microfluidic cartridge configured to receive a plurality of separate amplification-ready nucleic acid-containing samples at the plurality of separate sample inlets, each nucleic acid-containing sample associated with a microfluidic network of a plurality of microfluidic networks, each microfluidic network comprising an amplification region within which nucleic acid amplification is carried out when the nucleic-acid containing sample is received in the microfluidic cartridge, and 
 a plurality of disposable pipette tips; 
 
 a plurality of accessories comprising:
 a test strip carrier, and 
 a microfluidic cartridge carrier; and 
 
 an instrument comprising a touchscreen computer, a handheld barcode scanner, a keyboard, a mouse, and a power supply, the instrument further comprising:
 a receiving bay configured to receive a microfluidic cartridge of the plurality of multi-sample microfluidic cartridges, 
 a liquid-handling robot comprising a plurality of dispensing heads configured to transfer nucleic acid-containing samples to the plurality of separate sample inlets when the microfluidic cartridge is received in the receiving bay, 
 a plurality of separately controllable heat sources configured at the receiving bay, each heat source configured to thermal cycle a nucleic acid-containing sample in an amplification region of the microfluidic cartridge when received in the receiving bay, wherein the amplification region is maintained at a substantially uniform temperature at least once in each thermal cycle, 
 one or more processors configured to control the plurality of separately controllable heat sources when the microfluidic cartridge is received in the receiving bay, and 
 an optical scanner configured to measure a level of fluorescence emitted from each amplification region when the microfluidic cartridge is received in the receiving bay, the optical scanner further configured to provide real-time detection of an amplified target nucleic acid sequence in the respective amplification region, wherein the touchscreen computer is configured to display a test result for a nucleic-acid containing sample amplified in the microfluidic cartridge based at least in part on the level of fluorescence measured by the optical scanner. 
 
 
     
     
       2. The system of  claim 1 , wherein the system is configured for automated extraction and isolation of nucleic acids from multiple specimen types for a sample to result time of about one hour, with test results released continuously after the first test result. 
     
     
       3. The system of  claim 2 , wherein the optical scanner is configured to measure fluorescence at multiple wavelengths thereby enabling multiplexed detection in each amplification region in the microfluidic cartridge when received in the receiving bay. 
     
     
       4. The system of  claim 3 , wherein the plurality of separate sample inlets are aligned along a first axis of the microfluidic cartridge, wherein the amplification regions are aligned along a second axis substantially parallel to the first axis, and wherein the optical scanner does not cover the plurality of separate sample inlets when the microfluidic cartridge is received in the receiving bay. 
     
     
       5. The system of  claim 4 , wherein, when the microfluidic cartridge is received in the receiving bay, the liquid-handling robot is configured to transfer a nucleic acid-containing sample to the microfluidic cartridge after a different nucleic acid-containing sample has been amplified in the microfluidic cartridge. 
     
     
       6. The system of  claim 5 , wherein the liquid handling robot is configured to transfer a first plurality of nucleic acid-containing samples to a first set of separate sample inlets of the microfluidic cartridge when received in the receiving bay, and wherein the liquid handling robot is further configured to subsequently transfer a second plurality of nucleic acid-containing samples to a second set of separate sample inlets of the microfluidic cartridge after the first plurality of nucleic acid-containing samples has been amplified in the microfluidic cartridge. 
     
     
       7. The system of  claim 4 , further comprising a second receiving bay configured to receive a second microfluidic cartridge of the plurality of multi-sample microfluidic cartridges, wherein the system is configured to:
 concurrently process a first nucleic acid-containing sample in the microfluidic cartridge when received in the receiving bay and a second nucleic acid-containing sample in the second microfluidic cartridge when received in the second receiving bay; 
 consecutively process a third nucleic acid-containing sample in the microfluidic cartridge when received in the receiving bay and a fourth nucleic acid-containing sample in the second microfluidic cartridge when received in the second receiving bay; and 
 display a test result for the first, second, third, and fourth nucleic acid-containing samples on the touchscreen computer. 
 
     
     
       8. The system of  claim 7 , wherein the touchscreen computer is configured to display a test result for a nucleic-acid containing sample amplified in an amplification region of the microfluidic cartridge based at least in part on a level of fluorescence emitted from the amplification region by an amplified control nucleic acid sequence. 
     
     
       9. The system of  claim 8 , wherein the amplified target nucleic acid sequence is from an organism selected from the group consisting of: bacteria, a virus, human immunodeficiency virus, human papilloma virus, hepatitis B virus, hepatitis C virus, influenza virus, Group B  Streptococcus , Group A  Streptococcus, Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis , and  Mycoplasma genitalium.    
     
     
       10. The system of  claim 9 , wherein the system is configured to perform amplification and detection on 18 or more than 18 nucleic acid-containing samples in about an hour. 
     
     
       11. The system of  claim 10 , wherein, prior to performing real-time detection, the system is configured to perform a fill check to ensure that an amplification region is filled with a nucleic acid-containing sample when the microfluidic cartridge is received in the receiving bay and the nucleic-acid containing sample is transferred to the microfluidic cartridge. 
     
     
       12. The system of  claim 1 , wherein the optical scanner is configured to measure fluorescence at multiple wavelengths thereby enabling multiplexed detection in each amplification region in the microfluidic cartridge when received in the receiving bay. 
     
     
       13. The system of  claim 1 , wherein the plurality of separate sample inlets are aligned along a first axis of the microfluidic cartridge, wherein the amplification regions are aligned along a second axis substantially parallel to the first axis, and wherein the optical scanner does not cover the plurality of separate sample inlets when the microfluidic cartridge is received in the receiving bay. 
     
     
       14. The system of  claim 1 , wherein, when the microfluidic cartridge is received in the receiving bay, the liquid-handling robot is configured to transfer a nucleic acid-containing sample to the microfluidic cartridge after a different nucleic acid-containing sample has been amplified in the microfluidic cartridge. 
     
     
       15. The system of  claim 1 , wherein the liquid handling robot is configured to transfer a first plurality of nucleic acid-containing samples to a first set of separate sample inlets of the microfluidic cartridge when received in the receiving bay, and wherein the liquid handling robot is further configured to subsequently transfer a second plurality of nucleic acid-containing samples to a second set of separate sample inlets of the microfluidic cartridge after the first plurality of nucleic acid-containing samples has been amplified in the microfluidic cartridge. 
     
     
       16. The system of  claim 1 , further comprising a second receiving bay configured to receive a second microfluidic cartridge of the plurality of multi-sample microfluidic cartridges, wherein the system is configured to:
 concurrently process a first nucleic acid-containing sample in the microfluidic cartridge when received in the receiving bay and a second nucleic acid-containing sample in the second microfluidic cartridge when received in the second receiving bay; 
 consecutively process a third nucleic acid-containing sample in the microfluidic cartridge when received in the receiving bay and a fourth nucleic acid-containing sample in the second microfluidic cartridge when received in the second receiving bay; and 
 display a test result for the first, second, third, and fourth nucleic acid-containing samples on the touchscreen computer. 
 
     
     
       17. The system of  claim 1 , wherein the touchscreen computer is configured to display a test result for a nucleic-acid containing sample amplified in an amplification region of the microfluidic cartridge based at least in part on a level of fluorescence emitted from the amplification region by an amplified control nucleic acid sequence. 
     
     
       18. The system of  claim 1 , wherein the amplified target nucleic acid sequence is from an organism selected from the group consisting of: bacteria, a virus, human immunodeficiency virus, human papilloma virus, hepatitis B virus, hepatitis C virus, influenza virus, Group B  Streptococcus , Group A  Streptococcus, Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis , and  Mycoplasma genitalium.    
     
     
       19. The system of  claim 1 , wherein the system is configured to perform amplification and detection on 18 or more than 18 nucleic acid-containing samples in about an hour. 
     
     
       20. The system of  claim 1 , wherein, prior to performing real-time detection, the system is configured to perform a fill check to ensure that an amplification region is filled with a nucleic acid-containing sample when the microfluidic cartridge is received in the receiving bay and the nucleic-acid containing sample is transferred to the microfluidic cartridge.